rs1557072752
Variant summary
Our verdict is Likely pathogenic. Variant got 7 ACMG points: 7P and 0B. PVS1_StrongPM2PP5
The NM_006280.3(SSR4):c.187-301_352-15del variant causes a splice acceptor, splice donor, splice donor 5th base, coding sequence, intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (no stars).
Frequency
Genomes: not found (cov: 24)
Consequence
SSR4
NM_006280.3 splice_acceptor, splice_donor, splice_donor_5th_base, coding_sequence, intron
NM_006280.3 splice_acceptor, splice_donor, splice_donor_5th_base, coding_sequence, intron
Scores
Not classified
Clinical Significance
Conservation
PhyloP100: 2.06
Genes affected
SSR4 (HGNC:11326): (signal sequence receptor subunit 4) This gene encodes the delta subunit of the translocon-associated protein complex which is involved in translocating proteins across the endoplasmic reticulum membrane. The encoded protein is located in the Xq28 region and is arranged in a compact head-to-head manner with the isocitrate dehydrogenase 3 (NAD+) gamma gene and both genes are driven by a CpG-embedded bidirectional promoter. Alternate splicing results in multiple transcript variants.[provided by RefSeq, Mar 2011]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 7 ACMG points.
PVS1
?
Splicing variant, NOT destroyed by nmd, known LOF gene, truncates exone, which is 0.14176245 fraction of the gene. No cryptic splice site detected. Exon removal is inframe change.
PM2
?
Very rare variant in population databases, with high coverage;
PP5
?
Variant X-153797128-GGGCACCCCTGACCCCAGCACCTCCCTTGTAGACTCAGGAAATCACTCAGCCCTTTTGATCATCCCGCCCCTGCTCACAGTCAACAGGGTTCCTATGCGTCCAGTTAGGCCCGGCCATGGGGATCTGGCCTTGTGCCCCCGTAGGGAAGACCAATGCAGAGGGCCAGTCACGGGATTGGTGAGTGTTACTTGGTACCTCCTGCCAGGGACACTGCAGCCCCCAACTGGGCCTAGCCTGCCCACCTGCAGGCCGTGTGAGCAGCGCACAGGGCTCCTCTGCCCACACCCAGAGGGGGCAGAAGGTGACCCTGCCTTTGTTCCCTCACCCAGAACATGGCTCTCTATGCTGACGTCGGTGGAAAACAATTCCCTGTCACTCGAGGCCAGGATGTGGGGCGTTATCAGGTGAGGGGCCAATGGTTCCCTTGCTAGGGGGCTCCCTGCTCCCGGGTGTGACCTGAAGCCCCAGGGGTGGCCGGTCAACCAGGGCCAGGGGCCGTGGGCTCTGGCTGCCGGAGTGCTGCAGTGTCGGCACTGGTGGTCAGGGTGGCCCCTCCGTGTCCACTCTGCCCACACTCTGCTCAACACCCAACCCAGGTGTCCTGGAGCCTGGACCACAAGAGCGCCCACGCAGGCACCTATGAGGTTAGATTCTTCGACGAGGAGTCCTACAGCCTCCTCAGGAAGGTGAGGACTCCTGTAGCCCACTGTGCTCCCCTGTCCCTGGGGAGCAGGATGGGCTGGGTTGGGAGGTGCTGGCAGCAAGTCCTGAGCTGGGTGGCCTTTCTGTGATCCTGTCCCTTCCTCAGTGTCTCTTGCCCATTTCTCTCCTTTCCTTTTCTGGGGCTTGGGCCGGTGTTCCTACCTGTCTTTCCCCTCCCCTCCCCACCCCCACACGCCA-G is Pathogenic according to our data. Variant chrX-153797128-GGGCACCCCTGACCCCAGCACCTCCCTTGTAGACTCAGGAAATCACTCAGCCCTTTTGATCATCCCGCCCCTGCTCACAGTCAACAGGGTTCCTATGCGTCCAGTTAGGCCCGGCCATGGGGATCTGGCCTTGTGCCCCCGTAGGGAAGACCAATGCAGAGGGCCAGTCACGGGATTGGTGAGTGTTACTTGGTACCTCCTGCCAGGGACACTGCAGCCCCCAACTGGGCCTAGCCTGCCCACCTGCAGGCCGTGTGAGCAGCGCACAGGGCTCCTCTGCCCACACCCAGAGGGGGCAGAAGGTGACCCTGCCTTTGTTCCCTCACCCAGAACATGGCTCTCTATGCTGACGTCGGTGGAAAACAATTCCCTGTCACTCGAGGCCAGGATGTGGGGCGTTATCAGGTGAGGGGCCAATGGTTCCCTTGCTAGGGGGCTCCCTGCTCCCGGGTGTGACCTGAAGCCCCAGGGGTGGCCGGTCAACCAGGGCCAGGGGCCGTGGGCTCTGGCTGCCGGAGTGCTGCAGTGTCGGCACTGGTGGTCAGGGTGGCCCCTCCGTGTCCACTCTGCCCACACTCTGCTCAACACCCAACCCAGGTGTCCTGGAGCCTGGACCACAAGAGCGCCCACGCAGGCACCTATGAGGTTAGATTCTTCGACGAGGAGTCCTACAGCCTCCTCAGGAAGGTGAGGACTCCTGTAGCCCACTGTGCTCCCCTGTCCCTGGGGAGCAGGATGGGCTGGGTTGGGAGGTGCTGGCAGCAAGTCCTGAGCTGGGTGGCCTTTCTGTGATCCTGTCCCTTCCTCAGTGTCTCTTGCCCATTTCTCTCCTTTCCTTTTCTGGGGCTTGGGCCGGTGTTCCTACCTGTCTTTCCCCTCCCCTCCCCACCCCCACACGCCA-G is described in ClinVar as [Pathogenic]. Clinvar id is 372143.Status of the report is no_assertion_criteria_provided, 0 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
SSR4 | NM_006280.3 | c.187-301_352-15del | splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 3/6 | ENST00000370086.8 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
SSR4 | ENST00000370086.8 | c.187-301_352-15del | splice_acceptor_variant, splice_donor_variant, splice_donor_5th_base_variant, coding_sequence_variant, intron_variant | 3/6 | 1 | NM_006280.3 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 24
GnomAD3 genomes
?
Cov.:
24
We have no GnomAD4 exomes data on this position. Probably position not covered by the project.
GnomAD4 genome ? Cov.: 24
GnomAD4 genome
?
Cov.:
24
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:1
Revision: no assertion criteria provided
LINK: link
Submissions by phenotype
SSR4-congenital disorder of glycosylation Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | Nov 28, 2016 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at